This R-markdown document contains all r-code used to carry out the analysis for the paper on fish catch rates and species densities (species richness) along the Red Sea coast of Sudan. The analysis is based on three surveys: November 2012, May 2013 and November 2013.
Here the analysis is structured around the 7 management regions of the Sudanese Red Sea coast as follows:
All code and data are stored on GitHub
Reading catch, station and traits data.
Neither station data, nor catch data has a complete depth record, but by combining depth para from each we can get a complete depth parameter for all stations.
Loads the map data for Sudan, loads the management areas from shape-file etc.
## OGR data source with driver: ESRI Shapefile
## Source: "/Users/eriko/Documents/GitHub/Sudan2019/Sudan-master/sudan_management_areas", layer: "sudan_regions"
## with 7 features
## It has 3 fields
## Integer64 fields read as strings: id
Adds ‘Area’ to each line in the catch table.
Some more data wrangling that adds the traits from the traits table to the catch data, using only the station with catches (there are no traits for ‘NOCATCH’ species).
Also, only select traps, gillnets and handlines as these were the only gear with sufficient numbers and consistent use to be analyzed.
Lastly adds number of gear deployed at each station to each line.
Fig. 1 in MS
A nice, bathymetric map of Sudan with management areas overlaid.
Currently fonts and colours are adjusted for use on the ICES ASC 2019 poster, removing the bathy-contour lines (se ‘lwd’ to 0), and varying the colours of management area text to white for areas 1-4.
## quartz_off_screen
## 2